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- PDB-9rvu: in situ S. pombe hibernating ribosome after 7 days of glucose dep... -

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Basic information

Entry
Database: PDB / ID: 9rvu
Titlein situ S. pombe hibernating ribosome after 7 days of glucose depletion
Components
  • (Large ribosomal subunit protein ...) x 43
  • (Small ribosomal subunit protein ...) x 32
  • 18S small subunit ribosomal RNA
  • 28S large subunit ribosomal RNA
  • 5.8S large subunit ribosomal RNA
  • 5S large subunit ribosomal RNA
  • Elongation factor 2
  • Eukaryotic translation initiation factor 5A-1
  • Ribosome-associated protein oga1
  • SDO1-like protein C21C3.19
KeywordsRIBOSOME / SNOR / pombe / Yeast / Hibernating / Glucose / Cryo-ET / in-situ
Function / homology
Function and homology information


Peptide chain elongation / Hypusine synthesis from eIF5A-lysine / Synthesis of diphthamide-EEF2 / mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Platelet degranulation / Protein methylation / Protein hydroxylation ...Peptide chain elongation / Hypusine synthesis from eIF5A-lysine / Synthesis of diphthamide-EEF2 / mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Platelet degranulation / Protein methylation / Protein hydroxylation / regulation of cytoplasmic translational initiation in response to stress / RMTs methylate histone arginines / Neutrophil degranulation / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / ribonuclease MRP complex / translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of cytoplasmic translation / cytoplasmic translational elongation / GCN2-mediated signaling / positive regulation of translational termination / translation termination factor activity / translation activator activity / negative regulation of p38MAPK cascade / cytoplasmic translational termination / ribosome hibernation / positive regulation of translational elongation / preribosome / G-quadruplex DNA binding / tRNA processing / cytosolic large ribosomal subunit assembly / signaling receptor activator activity / negative regulation of translational frameshifting / ribosomal small subunit binding / TOR signaling / translational elongation / pre-mRNA intronic binding / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation elongation factor activity / protein-RNA complex assembly / maturation of LSU-rRNA / negative regulation of cytoplasmic translation / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-membrane adaptor activity / positive regulation of autophagy / rescue of stalled cytosolic ribosome / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of actin cytoskeleton organization / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / negative regulation of gene expression / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal ...Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Stm1-like, N-terminal / Stm1 / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / Ribosomal protein L28e / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / : / Ribosomal protein S26e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Elongation factor Tu domain 2 / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / 40S Ribosomal protein S10 / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / :
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS12A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS12A / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS7A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / Elongation factor 2 / Large ribosomal subunit protein eL19B / Large ribosomal subunit protein eL21B / Large ribosomal subunit protein uL13A / Ribosome-associated protein oga1 / Small ribosomal subunit protein eS17A / Small ribosomal subunit protein uS4B / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30C / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL18B / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL1B / Large ribosomal subunit protein eL24B / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL6B / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS1B / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein eL37B / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL39 / Ubiquitin-ribosomal protein eL40A fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL14A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS12A / Large ribosomal subunit protein uL5A / Small ribosomal subunit protein eS28A / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein eL30A / Eukaryotic translation initiation factor 5A-1 / Large ribosomal subunit protein uL15B / Small ribosomal subunit protein eS19A / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS25A / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL16A / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL23A / Large ribosomal subunit protein eL18B / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein eS6B / Large ribosomal subunit protein eL43A / Small ribosomal subunit protein eS4C / Small ribosomal subunit protein eS8B / SDO1-like protein C21C3.19 / Large ribosomal subunit protein eL34B / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL15B / Large ribosomal subunit protein eL38A / Large ribosomal subunit protein eL33A / Small ribosomal subunit protein eS26B / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS19B / Small ribosomal subunit protein uS2A
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3.38 Å
AuthorsRosa, H. / Gluc, M. / Jomaa, A. / Mattei, S.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nature / Year: 2026
Title: SNOR promotes translation restart after dormancy.
Authors: Maciej Gluc / Higor Rosa / Maria Bozko / Lesley A Turner / Cassidy R Prince / Yelena Peskova / Heather A Feaga / Kathleen L Gould / Simone Mattei / Ahmad Jomaa /
Abstract: Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains ...Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains unclear. Here, using high-resolution in situ cryo-electron tomography in Schizosaccharomyces pombe, we identify SNOR, an SBDS domain-containing ribosome-associated factor that binds at the peptidyl transferase centre and contacts the hypusinated loop of eIF5A during glucose depletion-induced dormancy. Rather than acting as a canonical hibernation factor, SNOR licenses dormant ribosomes for rapid translational restart. Upon glucose repletion, SNOR and eIF5A act together to promote efficient recovery of polysomes and exit from dormancy. These findings define a stress-responsive ribosome restart module that couples carbon-source limitation to surveillance of the ribosomal active site and reactivation of protein synthesis.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 18S small subunit ribosomal RNA
AD: Small ribosomal subunit protein uS2A
AE: Small ribosomal subunit protein eS1B
AF: Small ribosomal subunit protein uS5
AG: Small ribosomal subunit protein uS3
AH: Small ribosomal subunit protein eS4C
AI: Small ribosomal subunit protein uS7A
AJ: Small ribosomal subunit protein eS6B
AK: Small ribosomal subunit protein eS7
AL: Small ribosomal subunit protein eS8B
AM: Small ribosomal subunit protein uS4B
AN: Small ribosomal subunit protein eS10B
AO: Small ribosomal subunit protein uS17A
AP: Small ribosomal subunit protein eS12A
AQ: Small ribosomal subunit protein uS15
AR: Small ribosomal subunit protein uS11A
AS: Small ribosomal subunit protein uS19B
AT: Small ribosomal subunit protein uS9A
AU: Small ribosomal subunit protein eS17A
AV: Small ribosomal subunit protein uS13A
AW: Small ribosomal subunit protein eS19A
Aa: Small ribosomal subunit protein uS10
Ab: Small ribosomal subunit protein eS21
Ac: Small ribosomal subunit protein uS8A
Ad: Small ribosomal subunit protein uS12A
Ae: Small ribosomal subunit protein eS24A
Af: Small ribosomal subunit protein eS25A
Ag: Small ribosomal subunit protein eS26B
Ah: Small ribosomal subunit protein eS27
Ai: Small ribosomal subunit protein eS28A
Aj: Small ribosomal subunit protein uS14
Ak: Small ribosomal subunit protein eS30A
Am: Small ribosomal subunit protein RACK1
B0: Large ribosomal subunit protein eL42
B1: Large ribosomal subunit protein eL43A
B2: 28S large subunit ribosomal RNA
B3: 5S large subunit ribosomal RNA
B4: 5.8S large subunit ribosomal RNA
BN: Large ribosomal subunit protein uL2A
BO: Large ribosomal subunit protein uL3A
BP: Large ribosomal subunit protein uL4A
BQ: Large ribosomal subunit protein uL18B
BR: Large ribosomal subunit protein eL6
BS: Large ribosomal subunit protein uL30C
BT: Large ribosomal subunit protein eL8
BV: Large ribosomal subunit protein uL16A
BW: Large ribosomal subunit protein uL5A
BX: Large ribosomal subunit protein eL13
BY: Large ribosomal subunit protein eL14
BZ: Large ribosomal subunit protein eL15B
Ba: Large ribosomal subunit protein uL13A
Bc: Large ribosomal subunit protein eL18B
Bd: Large ribosomal subunit protein eL19B
Be: Large ribosomal subunit protein eL20A
Bf: Large ribosomal subunit protein eL21B
Bg: Large ribosomal subunit protein eL22
Bh: Large ribosomal subunit protein uL14A
Bi: Large ribosomal subunit protein eL24B
Bj: Large ribosomal subunit protein uL23A
Bk: Large ribosomal subunit protein uL24
Bl: Large ribosomal subunit protein eL27A
Bm: Large ribosomal subunit protein uL15B
Bn: Large ribosomal subunit protein eL29
Bo: Large ribosomal subunit protein eL30A
Bp: Large ribosomal subunit protein eL31
Bq: Large ribosomal subunit protein eL32A
Br: Large ribosomal subunit protein eL33A
Bs: Large ribosomal subunit protein eL34B
Bt: Large ribosomal subunit protein uL29
Bu: Large ribosomal subunit protein eL36B
Bv: Large ribosomal subunit protein eL37B
Bw: Large ribosomal subunit protein eL38A
Bx: Large ribosomal subunit protein eL39
By: Large ribosomal subunit protein eL28
H1: Ribosome-associated protein oga1
HE: Elongation factor 2
HL: Large ribosomal subunit protein uL1B
HS: SDO1-like protein C21C3.19
HI: Eukaryotic translation initiation factor 5A-1
BA: Large ribosomal subunit protein eL40A
BU: Large ribosomal subunit protein uL6B
Bb: Large ribosomal subunit protein uL22A
A: Large ribosomal subunit protein uL22A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,370,70189
Polymers3,370,30983
Non-polymers3926
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules AAB2B3B4

#1: RNA chain 18S small subunit ribosomal RNA


Mass: 593528.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#36: RNA chain 28S large subunit ribosomal RNA


Mass: 1129812.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
#37: RNA chain 5S large subunit ribosomal RNA


Mass: 78518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 157310380
#38: RNA chain 5.8S large subunit ribosomal RNA


Mass: 52880.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 1607200062

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Small ribosomal subunit protein ... , 32 types, 32 molecules ADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAaAbAcAdAeAfAgAhAiAjAkAm

#2: Protein Small ribosomal subunit protein uS2A / 40S ribosomal protein S0-A


Mass: 31794.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9Y7L8
#3: Protein Small ribosomal subunit protein eS1B / 40S ribosomal protein S1-B / S3aE-B


Mass: 28574.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94438
#4: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 27681.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74892
#5: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 27594.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60128
#6: Protein Small ribosomal subunit protein eS4C / 40S ribosomal protein S4-C


Mass: 29735.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P4W9
#7: Protein Small ribosomal subunit protein uS7A / 40S ribosomal protein S5-A


Mass: 22257.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14277
#8: Protein Small ribosomal subunit protein eS6B / 40S ribosomal protein S6-B


Mass: 27537.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9C0Z7
#9: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 21987.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10101
#10: Protein Small ribosomal subunit protein eS8B / 40S ribosomal protein S8-B


Mass: 22614.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7B2
#11: Protein Small ribosomal subunit protein uS4B / 40S ribosomal protein S9-B


Mass: 22290.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59675
#12: Protein Small ribosomal subunit protein eS10B / 40S ribosomal protein S10-B


Mass: 16470.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13614
#13: Protein Small ribosomal subunit protein uS17A / 40S ribosomal protein S11-A


Mass: 17535.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT73
#14: Protein Small ribosomal subunit protein eS12A / 40S ribosomal protein S12-A


Mass: 15632.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14062
#15: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 16985.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P28189
#16: Protein Small ribosomal subunit protein uS11A / 40S ribosomal protein S14-A


Mass: 14723.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT56
#17: Protein Small ribosomal subunit protein uS19B / 40S ribosomal protein S15-B


Mass: 17667.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTQ6
#18: Protein Small ribosomal subunit protein uS9A / 40S ribosomal protein S16-A


Mass: 15424.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT64
#19: Protein Small ribosomal subunit protein eS17A / 40S ribosomal protein S17-A


Mass: 15544.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42984
#20: Protein Small ribosomal subunit protein uS13A / 40S ribosomal protein S18-A


Mass: 17470.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT66
#21: Protein Small ribosomal subunit protein eS19A / 40S ribosomal protein S19-A / S16-A


Mass: 16178.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P58234
#22: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13569.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74893
#23: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21 / S28


Mass: 9627.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05764
#24: Protein Small ribosomal subunit protein uS8A / 40S ribosomal protein S22-A


Mass: 14785.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT58
#25: Protein Small ribosomal subunit protein uS12A / 40S ribosomal protein S23-A


Mass: 15691.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT75
#26: Protein Small ribosomal subunit protein eS24A / 40S ribosomal protein S24-A


Mass: 15506.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13784
#27: Protein Small ribosomal subunit protein eS25A / 40S ribosomal protein S25-A / S31-A


Mass: 9979.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79009
#28: Protein Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B


Mass: 13895.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTG4
#29: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27


Mass: 9185.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74330
#30: Protein Small ribosomal subunit protein eS28A / 40S ribosomal protein S28-A / S33


Mass: 7678.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT79
#31: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6672.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74329
#32: Protein Small ribosomal subunit protein eS30A / 40S ribosomal protein S30-A


Mass: 6928.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT62
#33: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein / Receptor of activated protein kinase C


Mass: 34887.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10281

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Large ribosomal subunit protein ... , 43 types, 43 molecules B0B1BNBOBPBQBRBSBTBVBWBXBYBZBaBcBdBeBfBgBhBiBjBkBlBmBnBoBpBq...

#34: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L42


Mass: 12239.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTI8
#35: Protein Large ribosomal subunit protein eL43A / 60S ribosomal protein L43-A / L37A


Mass: 10444.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HGL8
#39: Protein Large ribosomal subunit protein uL2A / 60S ribosomal protein L2-A / K37 / K5 / KD4


Mass: 27151.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT70
#40: Protein Large ribosomal subunit protein uL3A / 60S ribosomal protein L3-A / SP-L1


Mass: 43889.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P40372
#41: Protein Large ribosomal subunit protein uL4A / 60S ribosomal protein L4-A / L2


Mass: 39839.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P35679
#42: Protein Large ribosomal subunit protein uL18B / 60S ribosomal protein L5-B


Mass: 33538.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74306
#43: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 21285.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79071
#44: Protein Large ribosomal subunit protein uL30C / 60S ribosomal protein L7-C


Mass: 28780.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60143
#45: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L8 / L4 / L7A


Mass: 28659.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13672
#46: Protein Large ribosomal subunit protein uL16A / 60S ribosomal protein L10-A / QM protein homolog / SpQM


Mass: 25421.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09127
#47: Protein Large ribosomal subunit protein uL5A / 60S ribosomal protein L11-A


Mass: 19928.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT77
#48: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 23578.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74175
#49: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 15241.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94238
#50: Protein Large ribosomal subunit protein eL15B / 60S ribosomal protein L15-B / SP-L12


Mass: 23878.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9US22
#51: Protein Large ribosomal subunit protein uL13A / 60S ribosomal protein L16-A


Mass: 22050.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42848
#52: Protein Large ribosomal subunit protein eL18B / 60S ribosomal protein L18-B


Mass: 21234.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q8TFH1
#53: Protein Large ribosomal subunit protein eL19B / 60S ribosomal protein L19-B


Mass: 22813.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42699
#54: Protein Large ribosomal subunit protein eL20A / 60S ribosomal protein L20-A / SP-L17


Mass: 20642.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT68
#55: Protein Large ribosomal subunit protein eL21B / 60S ribosomal protein L21-B


Mass: 18390.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42706
#56: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 13344.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09668
#57: Protein Large ribosomal subunit protein uL14A / 60S ribosomal protein L23-A


Mass: 14905.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT60
#58: Protein Large ribosomal subunit protein eL24B / 60S ribosomal protein L24-B


Mass: 16957.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74884
#59: Protein Large ribosomal subunit protein uL23A / 60S ribosomal protein L25-A


Mass: 15870.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10330
#60: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 14375.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P78946
#61: Protein Large ribosomal subunit protein eL27A / 60S ribosomal protein L27-A


Mass: 15421.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14388
#62: Protein Large ribosomal subunit protein uL15B / 60S ribosomal protein L28-B


Mass: 16723.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P57728
#63: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / L43


Mass: 7224.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q92366
#64: Protein Large ribosomal subunit protein eL30A / 60S ribosomal protein L30-1 / L32


Mass: 11610.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P52808
#65: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 13290.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URX6
#66: Protein Large ribosomal subunit protein eL32A / 60S ribosomal protein L32-A


Mass: 14491.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79015
#67: Protein Large ribosomal subunit protein eL33A / 60S ribosomal protein L33-A / L37A


Mass: 12212.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USX4
#68: Protein Large ribosomal subunit protein eL34B / 60S ribosomal protein L34-2 / 60S ribosomal protein L34-B


Mass: 12828.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URT8
#69: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14333.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74904
#70: Protein Large ribosomal subunit protein eL36B / 60S ribosomal protein L36-B


Mass: 11287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94658
#71: Protein Large ribosomal subunit protein eL37B / 60S ribosomal protein L37-B / SP-L27


Mass: 10112.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05733
#72: Protein Large ribosomal subunit protein eL38A / 60S ribosomal protein L38-1


Mass: 8511.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USR7
#73: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 / SP-L36


Mass: 6326.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05767
#74: Protein Large ribosomal subunit protein eL28 / Probable 60S ribosomal protein L28e


Mass: 14781.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14069
#77: Protein Large ribosomal subunit protein uL1B / 60S ribosomal protein L1-B / L10a


Mass: 23959.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74836
#80: Protein Large ribosomal subunit protein eL40A / 60S ribosomal protein L40 / CEP52


Mass: 5960.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CH06
#81: Protein Large ribosomal subunit protein uL6B / 60S ribosomal protein L9-B


Mass: 21413.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74905
#82: Protein Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A


Mass: 20854.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14339
#83: Protein/peptide Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A


Mass: 2130.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14339

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Protein , 4 types, 4 molecules H1HEHSHI

#75: Protein Ribosome-associated protein oga1 / Ortholog of G4-associated protein 1 / Ribosome clamping factor oga1


Mass: 31007.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42914
#76: Protein Elongation factor 2 / EF-2


Mass: 93344.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14460
#78: Protein SDO1-like protein C21C3.19


Mass: 11909.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7K6
#79: Protein Eukaryotic translation initiation factor 5A-1 / eIF-5A-1


Mass: 17260.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P56289

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Non-polymers , 1 types, 6 molecules

#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: In situ cryo-ET Hibernating Ribosome from S. pombe under 7-day glucose depletion conditions
Type: RIBOSOME
Details: Full hibernating ribosome (Large and Small Subunits) with eEF2, eIF5a (with hypusination), SNOR (SBDS-domain containing hibernation factor), and Stm1.
Entity ID: #1-#83 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Objective Aperture 70 um
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Warp2.0.0dev36volume selectionWarpTools
2PHENIX1.21.2_5419model refinement
5Warp2.0.0dev36CTF correctionWarpTools
13Warp2.0.0dev363D reconstructionMTools
CTF correctionDetails: 3D CTF Estimation done in Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88206 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 715 / Num. of volumes extracted: 95485
RefinementHighest resolution: 3.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002224643
ELECTRON MICROSCOPYf_angle_d0.397328727
ELECTRON MICROSCOPYf_dihedral_angle_d20.96189031
ELECTRON MICROSCOPYf_chiral_restr0.02740960
ELECTRON MICROSCOPYf_plane_restr0.00322399

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